ENM 1.0
Home  |   DynOmics 1.0  |   Tutorials  |   Theory  |   References  |   iGNM 2.0  |   Mol. Sizer&Timer  |   ANM 2.0  |   Comp. Biol. Lab  |   PITT site

Reference List

ENM Theoretical Foundations
1.  Flory, P.J., Gordon, M. and McCrum, N.G. (1976) Statistical Thermodynamics of Random Networks [and Discussion]. Proceedings of the Royal Society of London. A. Mathematical and Physical Sciences, 351, 351-380
2.  Bahar, I., Atilgan, A.R. and Erman, B. (1997) Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential. Fold Des, 2, 173-181
3.  Haliloglu, T., Bahar, I. and Erman, B. (1997) Gaussian Dynamics of Folded Proteins. Physical Review Letters, 79, 3090-3093
4.  Bahar, I., Atilgan, A.R., Demirel, M.C. and Erman, B. (1998) Vibrational Dynamics of Folded Proteins: Significance of Slow and Fast Motions in Relation to Function and Stability. Physical Review Letters, 80, 2733-2736
5.  Atilgan, A.R., Durell, S.R., Jernigan, R.L., Demirel, M.C., Keskin, O. and Bahar, I. (2001) Anisotropy of fluctuation dynamics of proteins with an elastic network model. Biophys J, 80, 505-515
6.  Tama, F. and Sanejouand, Y.H. (2001) Conformational change of proteins arising from normal mode calculations. Protein Eng, 14, 1-6
Early extensions and applications
7.  Yang, L.W. and Bahar, I. (2005) Coupling between catalytic site and collective dynamics: a requirement for mechanochemical activity of enzymes. Structure, 13, 893-904
8.  Ming, D. and Wall, M.E. (2005) Allostery in a coarse-grained model of protein dynamics. Phys Rev Lett, 95, 198103
9.  Chennubhotla, C. and Bahar, I. (2007) Signal propagation in proteins and relation to equilibrium fluctuations. PLoS Comput Biol, 3, 1716-1726
10.Eyal, E. and Bahar, I. (2008) Toward a molecular understanding of the anisotropic response of proteins to external forces: insights from elastic network models. Biophys J, 94, 3424-3435
Recent extensions
11.Li, H., Sakuraba, S., Chandrasekaran, A. and Yang, L.W. (2014) Molecular binding sites are located near the interface of intrinsic dynamics domains (IDDs). J Chem Inf Model, 54, 2275-2285
12.Chandrasekaran, A., Chan, J., Lim, C. and Yang, L.W. (2016) Protein Dynamics and Contact Topology Reveal Protein-DNA Binding Orientation. J Chem Theory Comput, 12, 5269-5277
13.Eyal, E., Dutta, A. and Bahar, I. (2011) Cooperative dynamics of proteins unraveled by network models. Wiley Interdisciplinary Reviews: Computational Molecular Science, 1, 426-439
14.Yang, L.W. (2011) Models with energy penalty on interresidue rotation address insufficiencies of conventional elastic network models. Biophys J, 100, 1784-1793
15.Gur, M., Madura, J.D. and Bahar, I. (2013) Global transitions of proteins explored by a multiscale hybrid methodology: application to adenylate kinase. Biophys J, 105, 1643-1652
Web Servers/Databases
16.Lezon, T.R. and Bahar, I. (2012) Constraints imposed by the membrane selectively guide the alternating access dynamics of the glutamate transporter GltPh. Biophys J, 102, 1331-1340
17.Yang, L.W., Liu, X., Jursa, C.J., Holliman, M., Rader, A.J., Karimi, H.A. and Bahar, I. (2005) iGNM: a database of protein functional motions based on Gaussian Network Model. Bioinformatics, 21, 2978-2987
18.Yang, L.W., Rader, A.J., Liu, X., Jursa, C.J., Chen, S.C., Karimi, H.A. and Bahar, I. (2006) oGNM: online computation of structural dynamics using the Gaussian Network Model. Nucleic Acids Res, 34, W24-31
19.Li, H., Chang, Y.Y., Yang, L.W. and Bahar, I. (2016) iGNM 2.0: the Gaussian network model database for biomolecular structural dynamics. Nucleic Acids Res, 44, D415-422
20.Eyal, E., Yang, L.W. and Bahar, I. (2006) Anisotropic network model: systematic evaluation and a new web interface. Bioinformatics, 22, 2619-2627
21.Eyal, E., Lum, G. and Bahar, I. (2015) The anisotropic network model web server at 2015 (ANM 2.0). Bioinformatics, 31, 1487-1489
22.Yang, L.W., Eyal, E., Bahar, I. and Kitao, A. (2009) Principal component analysis of native ensembles of biomolecular structures (PCA_NEST): insights into functional dynamics. Bioinformatics, 25, 606-614
23.Bakan, A., Meireles, L.M. and Bahar, I. (2011) ProDy: protein dynamics inferred from theory and experiments. Bioinformatics, 27, 1575-1577
24.Bakan, A., Dutta, A., Mao, W., Liu, Y., Chennubhotla, C., Lezon, T.R. and Bahar, I. (2014) Evol and ProDy for bridging protein sequence evolution and structural dynamics. Bioinformatics, 30, 2681-2683
25.Yang, L.-W., Bahar, I., Rader, A.J. and Chennubhotla, C. (2005), Normal Mode Analysis. Chapman and Hall/CRC, pp. 41-64
26.Bahar, I. and Rader, A.J. (2005) Coarse-grained normal mode analysis in structural biology. Curr Opin Struct Biol, 15, 586-592
27.Haliloglu, T. and Bahar, I. (2015) Adaptability of protein structures to enable functional interactions and evolutionary implications. Curr Opin Struct Biol, 35, 17-23
28.Bahar, I., Cheng, M.H., Lee, J.Y., Kaya, C. and Zhang, S. (2015) Structure-Encoded Global Motions and Their Role in Mediating Protein-Substrate Interactions. Biophys J, 109, 1101-1109
29.Bahar, I. (2010) On the functional significance of soft modes predicted by coarse-grained models for membrane proteins. J Gen Physiol, 135, 563-573
30.Bahar, I., Lezon, T.R., Bakan, A. and Shrivastava, I.H. (2010) Normal mode analysis of biomolecular structures: functional mechanisms of membrane proteins. Chem Rev, 110, 1463-1497
31.Bahar, I., Lezon, T.R., Yang, L.W. and Eyal, E. (2010) Global dynamics of proteins: bridging between structure and function. Annu Rev Biophys, 39, 23-42